I’m new to writing macros and attempting to process a whole batch of images. After several processing steps I would like to apply a threshold to each image and have it be set such that the same percent of pixel intensities are thresholded every time. For reference, if you go to Image>Adjust>Threshold the box that comes up has a percent on the left side below the space with the slider graphic and histogram and you can see what percent of the pixels you are including/excluding.
I’ve found some different algorithms that could be used here: http://fiji.sc/Auto_Threshold and one might pass these along but as far as I can tell none are quite what I’m looking for in terms of approach. I’d like to either have the threshold dialog box just open for every image so I can set each image manually to the same percent thresholded, or ideally specify in the macro what threshold percentage should be used and just have it run that way. Any advice would be much appreciated!